Swarm v3: Towards tera-scale amplicon clustering

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Mahé, Frédéric, Czech, Lucas, Stamatakis, Alexandros, Quince, Christopher, de Vargas, Colomban, Dunthorn, Micah and Rognes, Torbjørn (2022) Swarm v3: Towards tera-scale amplicon clustering. Bioinformatics, 38 (1). pp. 267-269. ISSN 1367-4803

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Abstract

Motivation: Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) that are free of arbitrary global clustering thresholds. Here, we present swarm v3 to address issues of contemporary datasets that are growing towards tera-byte sizes. Results: When compared with previous swarm versions, swarm v3 has modernized C++ source code, reduced memory footprint by up to 50%, optimized CPU-usage and multithreading (more than 7 times faster with default parameters), and it has been extensively tested for its robustness and logic.

Item Type:	Article
Additional Information:	Acknowledgements: The authors thank Étienne Platini and Milena Königshoffen for writing unit tests, and Claude Monet for providing the impressionist background. The bioinformatics analyses were performed on the Core Cluster of the Institut Français de Bioinformatique (IFB) (ANR-11-INBS-0013). We are also grateful for access to computational resources provided by UNINETT Sigma2-the National Infrastructure for High Performance Computing and Data Storage in Norway (project NN9383K), the University of Oslo and the Oregon State University. Funding Information: This work was supported by the Gordon and Betty Moore Foundation through the UniEuk grant GBMF5275, the Klaus Tschira Foundation, and the Deutsche Forschungsgemeinschaft (#DU1319/5-1).
Uncontrolled Keywords:	statistics and probability,biochemistry,molecular biology,computer science applications,computational theory and mathematics,computational mathematics ,/dk/atira/pure/subjectarea/asjc/2600/2613
Faculty \ School:	Faculty of Science > School of Biological Sciences
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	29 Oct 2024 15:30
Last Modified:	31 Oct 2024 15:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/97344
DOI:	10.1093/bioinformatics/btab493

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